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To identify novel germline variants associated with breast cancer predisposition, whole-exome sequencing (WES) was performed.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>WES on 290<jats:italic>BRCA1\/BRCA2<\/jats:italic>-negative Singaporeans with early-onset breast cancer and\/or a family history of breast cancer was done. Case\u2013control analysis against the East-Asian subpopulation (EAS) from the Genome Aggregation Database (gnomAD) identified variants enriched in cases, which were further selected by occurrence in cancer gene databases. Variants were further evaluated in repeated case\u2013control analyses using a second case cohort from the database of Genotypes and Phenotypes (dbGaP) comprising 466 early-onset breast cancer patients from the United States, and a Singapore SG10K_Health control cohort.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Forty-nine breast cancer-associated germline pathogenic variants in 37 genes were identified in Singapore cases versus gnomAD (EAS). Compared against SG10K_Health controls, 13 of 49 variants remain significantly enriched (False Discovery Rate (FDR)-adjusted<jats:italic>p<\/jats:italic>\u2009&lt;\u20090.05). Comparing these 49 variants in dbGaP cases against gnomAD (EAS) and SG10K_Health controls revealed 23 concordant variants that were significantly enriched (FDR-adjusted<jats:italic>p<\/jats:italic>\u2009&lt;\u20090.05). Fourteen variants were consistently enriched in breast cancer cases across all comparisons (FDR-adjusted<jats:italic>p<\/jats:italic>\u2009&lt;\u20090.05). Seven variants in<jats:italic>GPRIN2, NRG1, MYO5A, CLIP1<\/jats:italic>,<jats:italic>CUX1, GNAS<\/jats:italic>and<jats:italic>MGA<\/jats:italic>were confirmed by Sanger sequencing.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>In conclusion, we have identified pathogenic variants in genes associated with breast cancer predisposition. Importantly, many of these variants were significant in a second case cohort from dbGaP, suggesting that the strategy of using case\u2013control analysis to select variants could potentially be utilized for identifying variants associated with cancer susceptibility.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s40246-022-00435-7","type":"journal-article","created":{"date-parts":[[2022,11,24]],"date-time":"2022-11-24T18:32:04Z","timestamp":1669314724000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Whole-exome sequencing of BRCA-negative breast cancer patients and case\u2013control analyses identify variants associated with breast cancer susceptibility"],"prefix":"10.1186","volume":"16","author":[{"given":"Ning Yuan","family":"Lee","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melissa","family":"Hum","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aseervatham Anusha","family":"Amali","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei Kiat","family":"Lim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"Wong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew Khine","family":"Myint","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ru Jin","family":"Tay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pei-Yi","family":"Ong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jens","family":"Samol","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chia Wei","family":"Lim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Ang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min-Han","family":"Tan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Soo-Chin","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ann S. 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M.-H.T. reports being a director, shareholder, and Chief Executive Officer of Lucence, outside of the submitted work. S.-C.L. reports grant support\/research collaborations with Pfizer, Eisai, Taiho, ACT Genomics, Bayer, and MSD; advisory board\/speaker invitations from Pfizer, Novartis, Astra Zeneca, ACT Genomics, Eli Lilly, MSD, Roche, Eisai and Daiichi-Sankyo; conference support from Amgen, Pfizer and Roche, all of which are outside the submitted work. All other authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"61"}}